Forest trees in general are out-crossing, long-lived, and at early stages of domestication. Molecular evolution at neutral sites is very slow because of the long generation times. Transferring information between closely related conifer species is facilitated by high sequence similarity. At the nucleotide level, trees have at most intermediate levels of variation relative to other plants. Importantly, in many species linkage disequilibrium within genes declines within less than 1000 bp. In contrast to the slow rate of neutral evolution, large tree populations respond rapidly to natural selection. Detecting traces of selection may be easier in tree populations than in many other species. Association studies between genotypes and phenotypes are proving to be useful tools for functional genomics.